Error with codeml

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Ying Huang

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Apr 21, 2016, 7:16:39 AM4/21/16
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Hi group,


I encoutered a problem when using codeml and couldn't solve it although I have went through related posts. So I post it here for help. The errors are shown in the following:

=================================================
  Error information
=================================================
Sequences read..
Counting site patterns..  0:00
         215 patterns at     1284 /     1284 sites (100.0%),  0:00
Counting codons..


      224 bytes for distance
   209840 bytes for conP
        0 bytes for fhK
  5000000 bytes for space
end of tree file.

Time used:  0:00

Data set 2

Reading options from ./test.ctl..



Error: seq err1: EOF.
seq file is not paml/phylip format.  Trying nexus format.
+++++++++++++++++++++end of the error information+++++++++++++++++++++

ps, I have checked my sequence file and ensure that there is 3 spaces (at least 2 spaces) between the sequence name and the sequence.

and paste part of my sequence data file in attanchment!



Thanks!
seq_data_file.png

Jeremy Chase

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Apr 22, 2016, 2:10:19 AM4/22/16
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I'm not sure about your format. This format works for me, so try it:

3 120
Species1
ATGGACCAGCCAGCTGGCCTGCAGGTGGACTACATCTTCCGGGGTGTGGAGCATGCCGTG
CGTGTGGTTGTTTCTGGGCAAGTGCTGGAGCTGGAGGTGGAGGACCGGATGACAGCTGAC
Species2
ATGGATCAGCCAGCTGGCCTGCAGGTGGACTACGTCTTCCGGGGTGTGGAGCATGCTGTG
CGTGTGGTGGTTTCTGGGCAAGTGCTGGAGCTGGAGGTGGAAGACCGGATGACAGCTGAC
Species3
ATGGATCAGCCAGCTGGCCTGCAGGTGGACTACGTCTTCCGGGGTGTGGAGCATGCTGTG
CGTGTGGTGGTTTCTGGGCAAGTGCTGGAGCTGGAGGTGGAAGACCGGATGACAGCTGAC

Ying Huang

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Apr 24, 2016, 9:16:21 PM4/24/16
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Hi Jeremy,

thanks for your suggestion. I have tried various file formats for codeml input file before searching for help, but it still didn't work. So I am trying to use other alignment tool (such as prank) to do MSA and then generate proper file format for codeml. 

Jeremy Chase

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Apr 25, 2016, 7:59:32 AM4/25/16
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I don't know if this is true, but I wonder if all the gaps in alignment are causing problems. Usually I use PRANK to do MSA and then use Gblocks to get gap-free alignments.

Good luck!

Ziheng

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Apr 30, 2016, 8:22:14 AM4/30/16
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the screen output says
Data set 2
Which indicates that the control file may be wrong. You should have ndata =1 and try again.
Perhaps try some example datasets first to get familiar with the program first.
Ziheng
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